Identification of virus species infecting sponge gourd in Zhejiang Province of China based on small RNA deep sequencing

doi:10.3969/j.issn.1004-1524.20250501

Acta Agriculturae Zhejiangensis ›› 2026, Vol. 38 ›› Issue (8): 1620-1627.DOI: 10.3969/j.issn.1004-1524.20250501

• Plant Protection • Previous Articles Next Articles

Identification of virus species infecting sponge gourd in Zhejiang Province of China based on small RNA deep sequencing

SHI Yujie¹^,²(), CHAI Yaqian¹^,², GAO Luyao¹, DONG Wenqi¹, ZHANG Peng¹, ZHOU Shengjun¹, WANG Xin¹, ZHU Yuqiang¹, SUN Yuyan¹^,^*()

¹ Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
² College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China

Received:2025-05-23 Online:2026-08-25 Published:2026-09-14

Abstract

Abstract:

To identify the virus species infecting sponge gourd in Zhejiang Province, small RNA deep sequencing technology was performed on two diseased sponge gourd leaves exhibiting typical viral symptoms collected from Jia-xing and Shaoxing, Zhejiang. The results showed that Tomato leaf curl New Delhi virus (ToLCNDV) was detected in the Jiaxing sample, while ToLCNDV, Cucurbit yellow stunting disorder virus (CYSDV) and Cucurbit chlorotic yellows virus(CCYV) were identified in Shaoxing sample. ToLCNDV was detected in both regions with high contig numbers and coverage. Phylogenetic analysis of the identified ToLCNDV DNA-A sequence indicated that the current pathogenic ToLCNDV in this study belongs to the Asian strain, with genetic evolution closely related to geographical regions, and cross-host transmission is widespread across regions. PCR detection of 37 samples from Zhejiang, Guangxi and Jiangxi revealed ToLCNDV detection rates of 87.5%, 60% and 100%, respectively. These results demonstrated that ToLCNDV had become a predominant virus in major sponge gourd production areas of Zhejiang and other provinces, warranting vigilance against the potential severe threat posed by its rapid spread and large-scale outbreaks to the luffa industry.

Key words: sponge gourd, small RNA deep sequencing, Tomato leaf curl New Delhi virus (ToLCNDV), virus

CLC Number:

S436.429

SHI Yujie, CHAI Yaqian, GAO Luyao, DONG Wenqi, ZHANG Peng, ZHOU Shengjun, WANG Xin, ZHU Yuqiang, SUN Yuyan. Identification of virus species infecting sponge gourd in Zhejiang Province of China based on small RNA deep sequencing[J]. Acta Agriculturae Zhejiangensis, 2026, 38(8): 1620-1627.

Figures/Tables 8

References 23

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用途 Usage	引物名称 Primer name	引物序列(5'→3') Primer sequence(5'→3')
DNA-A检测	ToLCNDV-A-61F	CCTATTTAATGCGTGGGGGT
Detection of DNA-A	ToLCNDV-A-1622R	AGCACTGAAGCAGTGGGCAA
验证测序结果准确性	ToLCNDV-A-F	TGCCTGCAGGTCGACTCTAGAACGTCTCCGTCTT
Verification of the accuracy of	ToLCNDV-A-R	TAAGAATTCGAGCTCGGTACCATGGGGTGTTTTCCAGATC
sequencing results	ToLCNDV-B-F	TGCCTGCAGGTCGACTCTAGAACTCAATCGGCGT
	ToLCNDV-B-R	TAAGAATTCGAGCTCGGTACCGAGAGAAACTGCTGCTTCT

用途 Usage	引物名称 Primer name	引物序列(5'→3') Primer sequence(5'→3')
DNA-A检测	ToLCNDV-A-61F	CCTATTTAATGCGTGGGGGT
Detection of DNA-A	ToLCNDV-A-1622R	AGCACTGAAGCAGTGGGCAA
验证测序结果准确性	ToLCNDV-A-F	TGCCTGCAGGTCGACTCTAGAACGTCTCCGTCTT
Verification of the accuracy of	ToLCNDV-A-R	TAAGAATTCGAGCTCGGTACCATGGGGTGTTTTCCAGATC
sequencing results	ToLCNDV-B-F	TGCCTGCAGGTCGACTCTAGAACTCAATCGGCGT
	ToLCNDV-B-R	TAAGAATTCGAGCTCGGTACCGAGAGAAACTGCTGCTTCT

样本 Sample	Read总数 Total reads	有效序列(占比/%) Clean read(proportion/%)	碱基总数 Base sum	GC含量/% GC content/%	N含量/% N content/%	Q30/%
嘉兴 Jiaxing	33 173 336	32 965 570(99.4)	735 041 593	45.86	0	97.39
绍兴 Shaoxing	34 473 140	34 269 880(99.4)	761 658 670	44.03	0.01	97.39

样本 Sample	Read总数 Total reads	有效序列(占比/%) Clean read(proportion/%)	碱基总数 Base sum	GC含量/% GC content/%	N含量/% N content/%	Q30/%
嘉兴 Jiaxing	33 173 336	32 965 570(99.4)	735 041 593	45.86	0	97.39
绍兴 Shaoxing	34 473 140	34 269 880(99.4)	761 658 670	44.03	0.01	97.39

样品来源 Sample source	比对序列 Reference sequence	测序总深度 (覆盖度/%) Total sequencing depth (coverage/%)	一致性/% Identity/%	重叠群数量 Contigs number	Contig长度/nt Contig length/nt	病毒 Virus	属 Genus	病毒类型 Virus type
嘉兴	HM007120	2 740 (100)	94.87	27	46~2 740	ToLCNDV	Begomovirus	DNA virus
Jiaxing	FN435312	2 696 (100)	96.08	28	41~1 424	ToLCNDV	Begomovirus	DNA virus
	MH465600	1 770 (65.4)	93.63	17	44~1 424	ToLCNDV	Begomovirus	DNA virus
绍兴	AJ620187	2 740 (100)	96.18	30	45~5 409	ToLCNDV	Begomovirus	DNA virus
Shaoxing	MH157025	2 738 (100)	96.79	31	45~5 409	ToLCNDV	Begomovirus	DNA virus
	FN435312	2 696 (100)	95.62	28	41~2 698	ToLCNDV	Begomovirus	DNA virus
	HG316125	2 577 (94.2)	97.01	30	46~5 409	ToLCNDV	Begomovirus	DNA virus
	MT813029	8 604 (94.4)	99.28	37	42~818	CYSDV	Crinivirus	RNA virus
	MT819949	7 489 (94.6)	99.27	22	45~1 266	CYSDV	Crinivirus	RNA virus
	AB523789	2 570 (32.0)	98.69	42	41~100	CCYV	Crinivirus	RNA virus
	MW629379	1 515 (17.6)	98.88	28	41~99	CCYV	Crinivirus	RNA virus

Identification of virus species infecting sponge gourd in Zhejiang Province of China based on small RNA deep sequencing

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